From 3d0116cad2a4b925d1ff829f8468049c5ea0363b Mon Sep 17 00:00:00 2001 From: MThomas91 Date: Fri, 4 Jul 2025 17:36:52 +0200 Subject: [PATCH 1/9] updated news --- NEWS.md | 8 ++++++++ 1 file changed, 8 insertions(+) diff --git a/NEWS.md b/NEWS.md index 3200ef7..fee32f1 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,11 @@ +# DoseFinding 1.4-1 +* Added powMCTInterim function to implement conditional/predictive power +calculations for interim analyses (#10) +* Added vignette illustrating analysis of longitudinal data (#29, thanks to Daniel Sabanes Bove for work on this and powMCTInterim) +* replaced uses of ggplot2::qplot, which is deprecated (#22) +* Minor updates to documentation and testing (#27 and #30) +* added hex sticker (#28) + # DoseFinding 1.3-1 * Added maFitMod function to implement fitting of dose-response models via model averaging (#11, thanks to Björn Bornkamp) From 5fd6bc89a81e5bfe9f0cf2f977157b282ab10025 Mon Sep 17 00:00:00 2001 From: MThomas91 Date: Mon, 7 Jul 2025 10:09:10 +0200 Subject: [PATCH 2/9] update description --- DESCRIPTION | 9 ++++++--- 1 file changed, 6 insertions(+), 3 deletions(-) diff --git a/DESCRIPTION b/DESCRIPTION index 010757f..89e9ccd 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,14 +1,17 @@ Package: DoseFinding Type: Package Title: Planning and Analyzing Dose Finding Experiments -Version: 1.3-1.9000 -Date: 2025-03-07 +Version: 1.4-1 +Date: 2025-07-07 Authors@R: c( - person("Bjoern", "Bornkamp", email = "bjoern.bornkamp@novartis.com", comment = c(ORCID = "0000-0002-6294-8185"), role = c("aut")), + person("Bjoern", "Bornkamp", email = "bjoern.bornkamp@novartis.com", + comment = c(ORCID = "0000-0002-6294-8185"), role = c("aut")), person("Jose", "Pinheiro", role = "aut"), person("Frank", "Bretz", role = "aut"), person("Ludger", "Sandig", role = "aut"), person("Marius", "Thomas", role = c("aut", "cre"), email = "marius.thomas@novartis.com"), + person("Daniel", "Sabanes Bove", role = "aut", email = "daniel.sabanes_bove@rconis.com", + comment = c(ORCID = "0000-0002-0176-9239")) person(given = "Novartis Pharma AG", role = c("cph", "fnd"))) Imports: ggplot2, lattice, mvtnorm Suggests: From d021658a0effd8b78e2fd8be3746661f7cad542f Mon Sep 17 00:00:00 2001 From: MThomas91 Date: Mon, 7 Jul 2025 10:16:14 +0200 Subject: [PATCH 3/9] fix description --- DESCRIPTION | 2 +- man/DoseFinding-package.Rd | 1 + 2 files changed, 2 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index 89e9ccd..d402a54 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -11,7 +11,7 @@ Authors@R: c( person("Ludger", "Sandig", role = "aut"), person("Marius", "Thomas", role = c("aut", "cre"), email = "marius.thomas@novartis.com"), person("Daniel", "Sabanes Bove", role = "aut", email = "daniel.sabanes_bove@rconis.com", - comment = c(ORCID = "0000-0002-0176-9239")) + comment = c(ORCID = "0000-0002-0176-9239")), person(given = "Novartis Pharma AG", role = c("cph", "fnd"))) Imports: ggplot2, lattice, mvtnorm Suggests: diff --git a/man/DoseFinding-package.Rd b/man/DoseFinding-package.Rd index 65a7180..6526cc9 100644 --- a/man/DoseFinding-package.Rd +++ b/man/DoseFinding-package.Rd @@ -98,6 +98,7 @@ Authors: \item Jose Pinheiro \item Frank Bretz \item Ludger Sandig + \item Daniel Sabanes Bove \email{daniel.sabanes_bove@rconis.com} (\href{https://orcid.org/0000-0002-0176-9239}{ORCID}) } Other contributors: From 615c43031903e954d4ffcd94d3689f13d7ec5f9f Mon Sep 17 00:00:00 2001 From: MThomas91 Date: Tue, 8 Jul 2025 13:37:00 +0200 Subject: [PATCH 4/9] use md syntax in powMCTInterim documentation --- R/powMCTInterim.R | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/R/powMCTInterim.R b/R/powMCTInterim.R index 9d9d5c5..5e426b7 100644 --- a/R/powMCTInterim.R +++ b/R/powMCTInterim.R @@ -5,7 +5,7 @@ #' interim data, e.g. for a futility interim analysis. This function can also be applied #' to longitudinal endpoints, where at the time of interim analysis incomplete data is #' available. For more details see the vignette on longitudinal data analysis with -#' MCP-Mod: \code{vignette("Longitudinal Data MCP-Mod", package = "DoseFinding")}. +#' MCP-Mod: `vignette("Longitudinal Data MCP-Mod", package = "DoseFinding")`. #' #' @inheritParams powMCT #' @param S_0t The covariance matrix for the first stage estimates From 4d49d3ca0fcfed060de9de993ec02848e9d0ba55 Mon Sep 17 00:00:00 2001 From: MThomas91 Date: Tue, 8 Jul 2025 16:05:56 +0200 Subject: [PATCH 5/9] update date --- DESCRIPTION | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index d402a54..fb2ca8f 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -2,7 +2,7 @@ Package: DoseFinding Type: Package Title: Planning and Analyzing Dose Finding Experiments Version: 1.4-1 -Date: 2025-07-07 +Date: 2025-07-08 Authors@R: c( person("Bjoern", "Bornkamp", email = "bjoern.bornkamp@novartis.com", comment = c(ORCID = "0000-0002-6294-8185"), role = c("aut")), From 6733520f976cb64f12b9b58eac04f07aca967df6 Mon Sep 17 00:00:00 2001 From: MThomas91 Date: Wed, 9 Jul 2025 17:54:25 +0200 Subject: [PATCH 6/9] add skips for long-running tests and vignette code --- cran-comments.md | 6 ++++++ tests/testthat/test-bMCTtest.R | 9 +++++++++ tests/testthat/test-sampSize.R | 3 +++ vignettes/longitudinal_data.Rmd | 2 +- 4 files changed, 19 insertions(+), 1 deletion(-) diff --git a/cran-comments.md b/cran-comments.md index 837203a..84d238a 100644 --- a/cran-comments.md +++ b/cran-comments.md @@ -1,3 +1,9 @@ +## Resubmission +This is a resubmission. In this version I have made the following updates to reduce check time + +* added skips for long running tests +* skipped evaluation for long-running vignette code + ## R CMD check results 0 errors | 0 warnings | 0 notes diff --git a/tests/testthat/test-bMCTtest.R b/tests/testthat/test-bMCTtest.R index ba4815f..8cd2309 100644 --- a/tests/testthat/test-bMCTtest.R +++ b/tests/testthat/test-bMCTtest.R @@ -207,6 +207,9 @@ test_that("unordered values in MCTtest work (unadjusted scale)", { }) test_that("bMCTtest gives same results as RBesT two-sample analysis with non-informative prior", { + skip_on_cran() + skip_on_ci() + require_rbest() set.seed(23) dd <- getDFdataSet_testsMCT() @@ -222,6 +225,9 @@ test_that("bMCTtest gives same results as RBesT two-sample analysis with non-inf test_that("bMCTtest gives same results as RBesT two-sample analysis with informative prior for control", { + skip_on_cran() + skip_on_ci() + require_rbest() set.seed(23) dd <- getDFdataSet_testsMCT() @@ -238,6 +244,9 @@ test_that("bMCTtest gives same results as RBesT two-sample analysis with informa }) test_that("bMCTtest gives same results as RBesT two-sample analysis with informative prior for both arms", { + skip_on_cran() + skip_on_ci() + require_rbest() set.seed(24) dd <- getDFdataSet_testsMCT() diff --git a/tests/testthat/test-sampSize.R b/tests/testthat/test-sampSize.R index 3bb41cd..f569c6c 100644 --- a/tests/testthat/test-sampSize.R +++ b/tests/testthat/test-sampSize.R @@ -17,6 +17,7 @@ tFunc <- function(n) { ######################################################### test_that("sampSize and sampSizeMCT work correctly", { + skip_on_cran() skip_on_ci() result1 <- sampSize(upperN = 80, targFunc = tFunc, target = 0.8, alRatio = rep(1, 6)) @@ -32,6 +33,7 @@ test_that("sampSize and sampSizeMCT work correctly", { }) test_that("sampSize and sampSizeMCT work correctly with Ntype = total", { + skip_on_cran() skip_on_ci() result1 <- sampSize(upperN = 80, targFunc = tFunc, target = 0.8, alRatio = rep(1, 6), Ntype = "total") @@ -47,6 +49,7 @@ test_that("sampSize and sampSizeMCT work correctly with Ntype = total", { }) test_that("sampSize and sampSizeMCT work correctly with sumFct = min", { + skip_on_cran() skip_on_ci() result1 <- sampSize(upperN = 80, targFunc = tFunc, target = 0.8, alRatio = rep(1, 6), Ntype = "total") diff --git a/vignettes/longitudinal_data.Rmd b/vignettes/longitudinal_data.Rmd index c894691..2a8c3bc 100644 --- a/vignettes/longitudinal_data.Rmd +++ b/vignettes/longitudinal_data.Rmd @@ -528,7 +528,7 @@ run_scen <- function(n_sim, rho, maxEff, These functions can be used as follows: -```{r} +```{r, eval = FALSE} doses <- c(0, 0.5, 1, 2, 4, 8) # doses alRatio <- c(2, 1, 1, 1, 2, 2) # allocation ratio for doses alpha <- 0.025 # for MCTtest From be4ce69b1ef262c8382ad9df03897a461898d8f5 Mon Sep 17 00:00:00 2001 From: MThomas91 Date: Thu, 10 Jul 2025 14:35:43 +0200 Subject: [PATCH 7/9] CRAN submission --- CRAN-SUBMISSION | 3 +++ 1 file changed, 3 insertions(+) create mode 100644 CRAN-SUBMISSION diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION new file mode 100644 index 0000000..1fdfcfd --- /dev/null +++ b/CRAN-SUBMISSION @@ -0,0 +1,3 @@ +Version: 1.4-1 +Date: 2025-07-09 15:58:40 UTC +SHA: 6733520f976cb64f12b9b58eac04f07aca967df6 From 68d7fa9d9c2f6e6580a9dd613e58dfdc99f186ba Mon Sep 17 00:00:00 2001 From: MThomas91 Date: Thu, 10 Jul 2025 14:37:56 +0200 Subject: [PATCH 8/9] github release --- CRAN-SUBMISSION | 3 --- 1 file changed, 3 deletions(-) delete mode 100644 CRAN-SUBMISSION diff --git a/CRAN-SUBMISSION b/CRAN-SUBMISSION deleted file mode 100644 index 1fdfcfd..0000000 --- a/CRAN-SUBMISSION +++ /dev/null @@ -1,3 +0,0 @@ -Version: 1.4-1 -Date: 2025-07-09 15:58:40 UTC -SHA: 6733520f976cb64f12b9b58eac04f07aca967df6 From 9b554b2f8b2c24092968c2644c96504ddd43dbd6 Mon Sep 17 00:00:00 2001 From: MThomas91 Date: Thu, 10 Jul 2025 14:39:10 +0200 Subject: [PATCH 9/9] update to dev version --- DESCRIPTION | 2 +- NEWS.md | 2 ++ 2 files changed, 3 insertions(+), 1 deletion(-) diff --git a/DESCRIPTION b/DESCRIPTION index fb2ca8f..d3cd9d3 100644 --- a/DESCRIPTION +++ b/DESCRIPTION @@ -1,7 +1,7 @@ Package: DoseFinding Type: Package Title: Planning and Analyzing Dose Finding Experiments -Version: 1.4-1 +Version: 1.4-1.9000 Date: 2025-07-08 Authors@R: c( person("Bjoern", "Bornkamp", email = "bjoern.bornkamp@novartis.com", diff --git a/NEWS.md b/NEWS.md index fee32f1..29cee38 100644 --- a/NEWS.md +++ b/NEWS.md @@ -1,3 +1,5 @@ +# DoseFinding (development version) + # DoseFinding 1.4-1 * Added powMCTInterim function to implement conditional/predictive power calculations for interim analyses (#10)